


Missing: One Lieutenant Colonel

by squidgie



Category: Stargate Atlantis
Genre: M/M
Language: English
Status: Completed
Published: 2016-09-05
Updated: 2016-09-05
Packaged: 2018-08-13 02:39:20
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 2,022
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7959109
Author URL: https://archiveofourown.org/users/squidgie/pseuds/squidgie
Summary: <blockquote class="userstuff">
              <p>Set post series finale, Rodney comes back from the SGC's Antarctic station to find John missing - and no one will tell him why.</p>
            </blockquote>





	Missing: One Lieutenant Colonel

**Author's Note:**

> Written for the StoryWork's community "Conspiracy" challenge. You can find the details here: http://story-works.livejournal.com/17080.html

Rodney yawned as he stepped off of the ‘jumper and back onto the deck of Atlantis.  After settling the city in San Francisco Bay, and then the quagmire of red tape that the SGC found to put them through before they could return to Pegasus, Rodney decided to spend some time at the SGC’s Antarctic station where he was able to get some uninterrupted time working on a backlog of projects.  And though it took him away from his normal routine – not to mention his time with John – he welcomed the distraction of actually working instead of wasting time in meetings and other non-productive happenings on the city that seemed to be becoming the norm now that they were stuck on Earth.

As he walked the warm metal of Atlantis’ decks past a bunch of Marines, Rodney glanced around, looking for but not seeing John amongst the skirmish of personnel that littered the area.  He figured John would be first one to play the Pegasus-imported version of Rugby, discovered after a trip to PK7-RP4.  The game was a quick hit with the Marines, as well as most Atlantis personnel.  John was often one of the first to suggest a game whenever there was downtime and energy to be worked off, because it not only helped keep the Marines sharp, but it required a lot less ammunition than hours of target practice.  As he walked by, he spotted a familiar face and called, “Cadman.  _Cadman_!” and then waved her over.

With a nod of acknowledgement, Laura Cadman called a timeout, then snatched the ball from one of the corporals before she sauntered over to where Rodney stood.  She blew a clump of sweaty hair out of her eyes, then dragged the strays back to the top of her head with her fingers as she came to stand next to Rodney.  “What’s up, McKay?  Welcome back.”  She was breathless from exertion and obviously tired, but she _still_ gave Rodney that slightly smarmy look that made him somewhat uncomfortable.

Ignoring the feeling as best he could, Rodney repositioned the duffle at his shoulder as he jutted his chin towards the crowd.  “Where’s John?”

And for the first time since Rodney had known her, Laura Cadman almost blanched, standing a bit straighter at the mention of John’s name.  “Dunno,” she said, her eyes suddenly looking around at everything else _but_ Rodney.

Cocking his head to the side, Rodney was about to question her when there was a call of “C’mon Lieutenant!” from the scrum.  “Okay...” Rodney replied, unsure of what to make of the situation.  “Well when was the last time you-“

Cadman just shook her head, and with a shrug of her shoulders, she turned and jogged back to where the Marines were gathered.

“Well that was...odd,” Rodney said to no one in particular.  He took one last glance around, then walked into the city.

Rodney’s first stop was the control room where he nodded to Chuck.  “Can I get a radio?” he asked.

“Welcome back, Doctor McKay,” Chuck replied with a smile.  Rodney watched as Chuck grabbed a radio from the charging station, noted the serial number, and then handed it over as he wrote it down in the equipment log.

“Thanks,” Rodney said as he flipped the switch, then placed it over his ear.  Positioning the microphone at his mouth, Rodney’s finger touched the transmit button and he called, “McKay to Sheppard.”

Before he can get a response, he heard Chuck say, “Oh,” in a tone of voice that clearly made the technician uncomfortable.  “Yeah, Umm, Doctor McKay?”

Rodney pointed to his earpiece, but got distracted when he saw Chuck shake his head.  “Yeah, you’re gonna want to talk to Mister Woolsey.”

Instantly Rodney’s mind reeled.  Had something happened since he left Atlantis three weeks prior?  Was John okay?  He let his imagination wander from John being in the infirmary, to court martialed, to worse.  “What’s going on, Chuck?” he asked, throat suddenly parched.  “Is John okay?”

“I...” Chuck stuttered.  “I’m afraid I can’t say, Doctor McKay.”

Rodney’s blood felt like it had turned to ice, and his stomach began to ache.  “Is he still on Atlantis?”

Chuck shook his head, though his words betrayed him when he replied, “I’m afraid I can’t say that, either.”

“So he’s _not_ in the city?”

Chuck looked as if he was suffering.  As the technician took a deep breath, he replied, “You _need_ to talk to Mister Woolsey.”

Rodney studied Chuck for a second and wondered what was going on.  It almost seemed as if John’s whereabouts was as concealed as the Stargate program.  Though Chuck and Cadman’s attitudes and actions had been odd, he hadn’t started to _truly_ worry.

That didn’t happen until Rodney barged into Woolsey’s office seconds later to confront Atlantis’ leader.  Woolsey, who had been in a meeting with several Stargate officials at the time clearly was uncomfortable, and not just at the intrusion.  He had bristled at the mention of John’s name, then stood and ushered Rodney out, saying he would talk to Rodney in due time.

By the time Rodney stormed into Lorne’s office, catching the Major off guard, his blood was boiling.  It was quite clear that _something_ had happened to John, but nobody would tell him.  He minced no words, and demanded, “Where is Colonel Sheppard?”

“Oh.  Rodney.  Welcome-“ was all that Lorne was able to get out.

“Don’t ‘Hi Rodney’ me!” he practically shouted at the Major.  “ _Where is John Sheppard_?”

Lorne did the same nervous glance that Cadman had earlier, which made Rodney’s blood pressure rise precipitously.  He opened his mouth to speak, but Rodney cut him off, saying, “There’s some damned conspiracy going on, and I’m tired of it.  Cadman.  Campbell.  Woolsey.” Rodney ticked off a finger with each spit of a new name.  “So consider your words carefully, Major Lorne, and tell me _exactly_ where Sheppard it.”

“I...  I _can’t_.” Lorne replied.

“Can’t or _won’t_?” Rodney demanded.

“Can’t,” Lorne clarified.

Rodney wiped his face in frustration.  “Is he at _least_ on Atlantis?”  When no indication came either way, he continued, “SGC?  California?  _Earth_?”

As he shook his head, Lorne replied, “Listen, Rodney.  I’m sorry, but I’m not able to-“

“Not able because – why – you’ve been ordered?” Rodney demanded.

Lorne looked as if he was a bit stuck, but finally – slowly – nodded his head.  “Affirmative, Doctor.”

“And you have been ordered to _not_ give me John’s whereabouts by...” Rodney prompted.

“Classified,” stonewalled Lorne.

“Then _fine_ ,” Rodney grumbled as he walked out of the office.  “Idiots.  I’m surrounded by _idiots_!”

Rodney marched to his quarters, tossed the few items he’d left on his bed weeks before to the floor, grabbed his laptop, and began the search for John.  

~*~*~

Sixteen hours later, still ensconced in his room and stonewalled by Atlantis staff, Rodney grew even more frustrated.  He’d run into dead-end after dead-end in his search for John.  Even after hacking records at the SGC, several commercial airlines that the SGC contracted with, and even train records, he found nothing.

Rodney glanced over at his duffle after his stomach grumbled a complaint for not having been fed.  He got up and stretched, then reached in and pulled a protein bar out of his bag, and sat back down with a thud.  His mind reeled at where to hack next in his search for John when his radio sounded in his ear.  “ _Woolsey to Doctor McKay_.”

He swatted his ear, then angrily responded, “McKay,” as he muttered, “About damned time.”

“ _You’re wanted on the West pier.  Woolsey out_.”

“God dammit,” Rodney grumbled, then tossed his laptop to the side.  “Not like I’m sitting here twiddling my damn thumbs.”  He stood, ripped the wrapper off the top of his powerbar in one smooth motion, and then lurched out his quarters towards the nearest transporter.  Between one chew and the next, the transporter conveyed him to the other side of the city.  He stomped out, then angrily pushed at the too-slow door and walked out into the setting sun.

And that’s where he found Lieutenant Colonel John Sheppard.  Standing on the deck of a sailboat, his sun-kissed skin practically glowing bronze, his messy hair tossed by the wind, and the biggest smile on his face.  “Hey, Rodney,” John called, then added a little wave.

Rodney very nearly tripped as he stumbled his way towards the sailboat.  Several thoughts fought for the right neural pathway between his brain and his mouth.  After a few failed attempts of, “But,” and “Oh, and, “What?” Rodney finally settled on a concise stream of words.  “John Patrick Sheppard, would you mind telling me just exactly _what_ the ever-loving hell is going on?”

“Thirteen hundred hours,” is all John cryptically replied.  Which only served to make Rodney even _more_ frustrated. 

John put his hands on his hips, pulling the pants up as they tried to slink down past his bony hips.  Hips that Rodney had spent many a night clinging to, in passion or just in slumber.  Hips that, even now, tried to garner Rodney’s attention.

“Thirteen hundred-“

“You said that already,” Rodney balked.  “What the hell is thirteen hundred hours, and what does it have to do with the monumental secrecy around where you’ve been.  And what the hell does _that_ have to do with you standing on the deck of a damn sailboat?”

“How long were we in Pegasus, Rodney?” John asked.  But John didn’t wait for Rodney respond, and said, “Five and a half years.  And what’s the standard vacation time compensation for SGC personnel?”  Again without waiting, he responded, “Six weeks per year, or 4.62 hours per week.  And since it has been approximately five and a half years since we first went to Pegasus, and _none of us_ – not me, not you, none – have taken even an hour’s worth of vacation, that means you have approximately thirteen hundred hours of vacation saved up.”

Rodney suddenly felt deflated, every bit of anger and worry suddenly disappearing into the atmosphere.  He shook his head and couldn’t help but smile as John walked to the port side of the sailboat.  Steading himself on the deck, John grabbed the rope that moored it to Atlantis, and Rodney watched as John’s free hand gestured for him to come towards the boat.

“You wanna?” John asked, then reached out his hand to beckon Rodney aboard.

Rodney reached out and took John’s hand, then stepped across the gap where he came to stand on the deck of John’s sailboat, John’s strong arms coming around him.

“You’re insane.  You know that?” Rodney asked after he stole a quick kiss.

“Yeah,” John replied.  “But you love me anyway.”

It wasn’t until hours later, after they’d cast off from Atlantis for ‘parts unknown’ as John told it, that Rodney realized he didn’t have, “Anything.  I mean no clothes.  No laptop.  No...sunscreen.”

“First of all, I stole that big-ass jar of sunscreen that you kept in your quarters.  It’s down in the stores.”

“Seriously?” Rodney asked.  “And why all the secrecy?”

“I didn’t want you to bitch at me and try and get out of it.  So I only told a couple of people – and even them, I only told a little bit of my plan.  Threatened all my direct reports with KP duty for a month if they so much as uttered a word of my plan.”  With a wink in his eye, he added, “Threatened Woolsey that we’d both bail on the SGC if he said a word.”

Rodney couldn’t help but grin at John’s admission.

“And lastly,” John said, then paused to tug Rodney to him.  He put one hand on the back of Rodney’s neck and pulled him forward, kissing him with just enough heat to make Rodney groan, though based on the firmness Rodney felt at his thigh, Rodney wasn’t the only one happy with John’s plan. 

When John finally broke the kiss, he leaned his forehead against Rodney’s, the two grinning at each other as the moonlight danced on the ocean around them.  “You think we’re _really_ gonna need clothes on this vacation?”


End file.
